Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma

Mol Cell Proteomics. 2011 Dec;10(12):M111.009290. doi: 10.1074/mcp.M111.009290. Epub 2011 Sep 22.


A simple mass spectrometric approach for the discovery and validation of biomarkers in human plasma was developed by targeting nonglycosylated tryptic peptides adjacent to glycosylation sites in an N-linked glycoprotein, one of the most important biomarkers for early detection, prognoses, and disease therapies. The discovery and validation of novel biomarkers requires complex sample pretreatment steps, such as depletion of highly abundant proteins, enrichment of desired proteins, or the development of new antibodies. The current study exploited the steric hindrance of glycan units in N-linked glycoproteins, which significantly affects the efficiency of proteolytic digestion if an enzymatically active amino acid is adjacent to the N-linked glycosylation site. Proteolytic digestion then results in quantitatively different peptide products in accordance with the degree of glycosylation. The effect of glycan steric hindrance on tryptic digestion was first demonstrated using alpha-1-acid glycoprotein (AGP) as a model compound versus deglycosylated alpha-1-acid glycoprotein. Second, nonglycosylated tryptic peptide biomarkers, which generally show much higher sensitivity in mass spectrometric analyses than their glycosylated counterparts, were quantified in human hepatocellular carcinoma plasma using a label-free method with no need for N-linked glycoprotein enrichment. Finally, the method was validated using a multiple reaction monitoring analysis, demonstrating that the newly discovered nonglycosylated tryptic peptide targets were present at different levels in normal and hepatocellular carcinoma plasmas. The area under the receiver operating characteristic curve generated through analyses of nonglycosylated tryptic peptide from vitronectin precursor protein was 0.978, the highest observed in a group of patients with hepatocellular carcinoma. This work provides a targeted means of discovering and validating nonglycosylated tryptic peptides as biomarkers in human plasma, without the need for complex enrichment processes or expensive antibody preparations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Amino Acid Sequence
  • Biomarkers, Tumor / blood*
  • Biomarkers, Tumor / chemistry
  • Biomarkers, Tumor / isolation & purification
  • Carcinoma, Hepatocellular / blood*
  • Carrier Proteins / blood
  • Carrier Proteins / chemistry
  • Carrier Proteins / isolation & purification
  • Chromatography, High Pressure Liquid
  • Female
  • Glycoproteins / blood*
  • Glycoproteins / chemistry
  • Glycoproteins / isolation & purification
  • Glycosylation
  • Humans
  • Kininogens / blood
  • Kininogens / chemistry
  • Kininogens / isolation & purification
  • Liver Neoplasms / blood*
  • Male
  • Middle Aged
  • Molecular Sequence Data
  • Orosomucoid / chemistry
  • Peptide Fragments / chemistry*
  • Peptide Fragments / isolation & purification
  • Peptide Fragments / standards
  • ROC Curve
  • Reference Standards
  • Serum Albumin / chemistry
  • Serum Albumin / isolation & purification
  • Serum Albumin, Human
  • Tandem Mass Spectrometry / standards
  • Trypsin / chemistry*
  • Vitronectin / blood
  • Vitronectin / chemistry
  • Vitronectin / isolation & purification


  • AFM protein, human
  • Biomarkers, Tumor
  • Carrier Proteins
  • Glycoproteins
  • Kininogens
  • Orosomucoid
  • Peptide Fragments
  • Serum Albumin
  • Vitronectin
  • Trypsin
  • Serum Albumin, Human